In a response to publication of the Cheng, et al paper in PNAS which demonstrated an evolutionary pathway to the antifreeze gene that protects fish from freezing in Antarctic water (see also my post on it), Casey Luskin, attack gerbil of the Disco ‘Tute, invokes Stephen Jay Gould’s infamous “just so” phrase. Luskin then kindly outlines the three steps in constructing a “just so” story to account for biological phenomena. Here I’ll walk through Casey’s steps for a parallel case to show just how specious his claim is. The parallel case is accounting for how a particular boulder, indicated below by the red arrow, got to where it was in a landslide (image used by permission of Air-and-Space Museum).

Luskin’s main complaint about the Cheng, et al. paper is that it invokes various processes (known to occur in nature) to account for the end product:

[It claims that] AFPIII evolved from a duplicate copy of another gene in the fish, SAS-B. They summarize their evolutionary story: “AFPIII 5’FR, intron1 (I1), exon2 (E2; icebinding mature AFPIII), and 3’FR were derived from the 5’FR, I5, E6 (SAS C-terminal domain), and 3’FR, respectively, of the ancestral LdSAS-B,” and then “[a]ccelerated adaptive changes subsequently occurred in the nascent AFPIII gene.”

The Gene Evolution Game
Sounds simple and compelling, right? Don’t be too impressed. If you go back and read my article, “How to Play the Gene Evolution Game,” you’ll find that by using a combination of three magic wands – Gene Duplication, Natural Selection, and Rearrangement – it’s a simple matter to concoct a just-so story to “explain” the origin just about any gene sequence – no details required:

Let me walk through the steps of Luskin’s Game, translating to show how they would operate in the boulder/landslide scenario.

Gene Evolution Game Rule 1: Whenever you find sequence homology between two genes, just invoke a duplication event of some hypothetical, ancient ancestral gene, and you can explain how two different genes came to share their similarities.

For the boulder that translates to something like

Boulder Game Rule 1: Whenever you find shape and mineral composition homology between a rock at the bottom of a slope and a ledge up the slope, just invoke a hypothetical breakage event and a hypothetical landslide event and you can explain how the rock and the ledge come to share their similarities in shape and composition.

So if we search the cliff above the landslide and find a ledge that has a similar mineral composition and find a portion of the ledge with a physical shape at its edge that’s roughly complementary to the shape of a side of the boulder, we just invoke hypothetical breakage and landslide events to account for the boulder’s existence and position, using the magic wand of gravity as a natural law in our explanation.

Second, Luskin tells us

Gene Evolution Game Rule 2: When you need to explain how a gene acquired some new function, or evolved differences from another gene, just invoke the magic wand of natural selection.

In our boulder example, that translates to

Boulder Game Rule 2: When you need to explain how a boulder acquired some nicks and chips or shape differences from the ledge above just invoke the magic wand of collisions with other boulders during the hypothetical landslide. To account for the driving force that got it to its position at the bottom of the slope just invoke the magic wand of gravity.

Finally, Luskin’s third rule is

Gene Evolution Game Rule 3: When a gene seems to be composed of the parts of several genes, just invoke duplications and rearrangements of all the DNA sequences you need, so you can get them all together in the right place.

That translates to

Boulder Game Rule 3: When a boulder has surface marks of a different composition than the original ledge, just invoke collisions with boulders of a different composition during the hypothetical landslide to account for the marks, and maybe even find the other boulders that contributed the marks. Of course you’ll also have to invoke hypothetical friction and hypothetical collisions, along with the magic wand of gravity again.

Luskin goes on to critique the paper for not reaching the IDist’s favorite and most distant goalpost:

While previous studies had identified some of the supposedly “positively selected” amino acids as important to the antifreeze function, the authors make no attempt to provide a step-by-step explanation of how SAS-B’ changed into AFPIII.

As is obvious, in Luskin’s twisted world we can’t satisfactorily account for the boulder’s structure, appearance, and position merely by invoking known physical laws (gravity) and processes (rock breakage and collisions and friction). We have to give a centimeter-by-centimeter, bounce-by-bounce, collision-by-collision description of the descent of that particular boulder before Luskin will believe that the boulder’s source is the ledge above and that its final position and appearance are due to the vicissitudes of boulders tumbling downhill in landslides powered by gravity. That’s the goalpost Michael Behe and all IDists move to whenever they’re confronted with an account like that in the Cheng, et al. paper or, for that matter, in our landslide example. For Luskin, the “magic wands” of gravity and the presence of other components of the landslide together with random bounces during a landslide that are no longer accessible to direct inspection cannot explain the position and appearance of the boulder in the image: It’s perfectly obvious that we have to invoke Intelligent Falling.

“Things fall not because they are acted upon by some gravitational force, but because a higher intelligence, ‘God’ if you will, is pushing them down,” said Gabriel Burdett, who holds degrees in education, applied Scripture, and physics from Oral Roberts University.

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244 Comments

Well, a “just so” story is a lot better than the Luskin alternative, a “just not so” story.

OK Casey, how do you explain sequence homology between genes? Coincidence? Intelligent design? That doesn’t even make any sense of course.

This argument amounts to “were you there”? If we don’t actually see the gene duplication happen, then it is assumed that it could not happen. No matter how much evidence there is that it actually did happen. And of course if we ever did actually observe it happen, then it happened in the lab and not in nature, so that doesn’t count!

Unless we actually see the rock fall, it couldn’t fall. And if we actually do see the rock w=fall, we must have done something to make it fall, so that doesn’t count! Heads I win, tails I hit you on the head with the rock.

We have to give a centimeter-by-centimeter, bounce-by-bounce, collision-by-collision description of the descent of that particular boulder before Luskin will believe that the boulder’s source is the ledge above and that its final position and appearance are due to the vicissitudes of boulders tumbling downhill in landslides powered by gravity.

In his 2005 textbook Evolution, Douglas Futuyma states that a high estimate of the gene duplication rate is “about 0.01 duplication per gene per million years.” (p. 470) A given gene will thus be duplicated about once every 100 million years. The present paper speculates that the antifreeze gene evolved in response to cooling temperatures in the Antarctic deep ocean water over the past 50 million years. What are we to make, then, of the fact that Antarctic eelpouts have over 30 AFPIII genes, all of which are said to have resulted from a duplication of a single AFPIII gene which evolved at some point in the past 50 million years in response to changing ocean temperatures?

Sorry I forgot the end.…More of Casey Luskin about AFPIII gene duplications.

Even if one invokes the magic wand of “positive selection,” this gene was apparently duplicating at a rate far higher than the average gene duplication rate. It should have taken some 3 billion years just to accomplish the last step of this little story, which took place in far less than 50 million years, as these repeated duplications are the very last step of the story. In other words, in the last stage alone it seems that this paper requires far too much genetic evolutionary change too quickly.

While I have little doubt in my mind that the vast majority of what Luskin writes is clownish in the extreme, would you mind, for those of us playing along at home, explaining what is wrong with this particular argument?

While I have little doubt in my mind that the vast majority of what Luskin writes is clownish in the extreme, would you mind, for those of us playing along at home, explaining what is wrong with this particular argument?

Dave C – what RBH and Tiel said, plus the first gene duplication often makes a second duplication more likely, and a second duplication makes additional duplications even more likely, so you get a “snowball” effect.

For Dave C here’s a back-of-the-eyeball calculation to illustrate what Tiel and I meant. (Somebody check my math: I’m subject to “chemotherapy brain” and am doing it in my head.)

Say there are 10,000,000 eelpouts (Cheng’s icefish) in the Antarctic population, each with 25,000 genes (not unrealistic numbers). That’s 250,000,000,000 genes in the population at any given time. At a gene duplication rate of 0.01 per gene per 1,000,000 years, we expect to see 2,500 gene duplications in the population every year, or one duplication in every 4,000 fish per year. In 10 years, assuming no biases regarding which genes duplicate, it’s possible that every gene of the 25,000 in the eelpout genome will have duplicated at least once in at least one fish. In 1,000 years it’s practically certain that every gene will have been duplicated at least once in at least one fish. Thereafter it’s up to natural selection and genetic drift, both of which are known to operate, kind of like the magic wand of gravity. :)

And yet, whenever I ask Intelligent Design proponents or Creationists why we’re supposed to blindly assume that saying “God/Intelligent Designer poofed it with magic” is supposed to be more scientific than actual science, they always act like I made a maliciously unpleasant comment about their mothers.

And there’s more than one gene in a genome. Casey Luskin forgets what a “mean” is…

Is Futuyma’s rate a mutation rate for the gene duplication type of mutation? (If so, it seems way too low.) Or is it some kind of average rate of increase of total genes in a lineage from the Precambrian til now…

Henry J said:
Say there are 10,000,000 eelpouts (Cheng’s icefish) in the Antarctic population, each with 25,000 genes (not unrealistic numbers). That’s 250,000,000,000 genes in the population at any given time. At a gene duplication rate of 0.01 per gene per 1,000,000 years, we expect to see 2,500 gene duplications in the population every year, or one duplication in every 4,000 fish per year. In 10 years, assuming no biases regarding which genes duplicate, it’s possible that every gene of the 25,000 in the eelpout genome will have duplicated at least once in at least one fish. In 1,000 years it’s practically certain that every gene will have been duplicated at least once in at least one fish. Thereafter it’s up to natural selection and genetic drift, both of which are known to operate, kind of like the magic wand of gravity. :)

Thanks, that illustration was helpful. It seems like this type of thing should be obvious to anyone remotely familiar with population genetics. I wonder how long it will take for Luksin to wise up and edit that part out of the article…

So Casey’s basically offering up a version of the old “how can you prove it happened if you weren’t there to see it” argument (with the creationist corollary “… and if you can’t prove it happened, then Goddidit”).

Sorry, this comment is related to another story which PT covered earlier, the ARK in Kentucky, but Ken Ham is just as disgusting regarding creationism as Luskin. It’s an interview with Ken Ham & Barry Lynn regarding the public funding of the ARK project.

Mr Luskin has given a perfect example of the arguments presented by most creation “science”. It is not about carefully checking facts and conclusions it is about presenting an argument that will convince the villagers (in other words a good story). So maybe someone should grab these papers and have them loosely translated by a good fictional writer ;)

Luskin’s argument is too crude to merit the name of sophistry. By calling natural selection a “magic wand,” he is assuming the very point he is trying to prove–that evolution by natural selection is a false or incomplete explanation of speciation.

In other words, stripped of pseudo academic flourishes, his entire argument is founded upon question begging. We can ignore the fiddly-bits, leaving more time to marvel at the dishonesty of the IDeist mind.

The duplication and billion years thing - there might be duplications all the time, but there is no positive selection for them and they are lost (reaching only a rare population frequency that we don’t spot), like a red headed orphan raised in Tibet. How many generations would that red headed trait last in the population?

Also, many of those (partial)duplications are harmful - Down’s syndrome, many cancers. Posters at ASHG are loaded with photos of kids and embryos with chromosomal mutations that leave them deformed or dead. It’s extremely common, but these traits are negatively selected.

So it’s not a billion years to get a beneficial mutation, it’s only every billion years that an environmental condition AND a duplication of ONE gene act to favorably select that gene. But when the conditions change and new traits are needed, natural selection promotes them from the ranks.

Or to put it more familiar terms - by the end of ww2, you could become a Luftwaffe pilot in a couple weeks because the death rate was so high. Sometimes there’s nothing like tremendous mayhem to send positive selection into overdrive.

And unfortunately with the boulder analogy, God never gives us proof of his divine guidance, like having those boulders spontaneously assemble into a nice bungalow at the base of the cliff.

Nope, Irreducible Complexity only gets invoked as a convenient attack on scientific theories. Where is it other times? Where are the spontaneously formed houses? How could God be so careless as to not do that for us? Where are the clouds in the perfect shapes of Euclidean solids? Why aren’t any of the Great Lakes in the perfectly detailed outline of a pony? Why don’t butterfly wings have Bible verses on them?

Back to that scenario about children with chromsomal duplications or deletions - these traits can be recessive, so when you see one of these cases and they show the pedigree of some family from an isolated population like a village in Malta, you see that the child is the result of the kids gandparents being cousins and the father married his own aunt. Natural selection in a large population only reveals these duplications rarely, but just a little selection (such as inbreeding) in an isolated population shows that the actual rate of gene rearrangements is much much higher than you would suspect, and thus cousins should not marry. And when conditions change, there are lots of mutations available to be selected, and probably a population bottleneck that will swiftly increase the allelic frequency of the mutation.

If mutations were as rare as the ID people imply, there would no harm in siblings marrying each other generation after generation, and even illiterate nomads know more science than that.